Most people don't really like Index in Toaru Majutsu no Index. They are all just fan boying over BiriBiri.
Aswell as the childhood friends thing. Most avid romance fans always know that it is rare to have the childhood friend route even touched, they always end up as a side character to help with main love interest. That's why we usually cheer for childhood friend even if it never comes through, screw that random transfer girl.
Would be nice to see that school president girl from Inou-Battle more often. Made such a huge impression in episode two and basically died out, never to return again.
There is also Angel Beats that I wished had more time to go over the story of each characters. However the anime was too short for that, but the VN is coming out soon with stories for every character, however long it'll probably take to translate it.
Clannad aswell, I wished for more Kyou and Tomoya time, however they went a different route, though there is already a green light for the Clannad VN to come out on Steam later on.